


Flipped

by quinjjet



Category: Agents of S.H.I.E.L.D. (TV)
Genre: AKA, Alternate Universe - Different Framework Universe (Marvel), Angst, Madame Jemma Simmons, My Framework, POV First Person, Visions in dreams, what I high-key wanted to happen
Language: English
Status: In-Progress
Published: 2020-11-28
Updated: 2020-12-15
Packaged: 2021-03-10 00:00:21
Rating: Not Rated
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 4
Words: 4,174
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/27744862
Author URL: https://archiveofourown.org/users/quinjjet/pseuds/quinjjet
Summary: A.I.D.A messed up something in the programming of the framework. She was trying to make Fitz's feeling for Jemma about her, but she accidentally flipped their roles. So when Jemma get's plugged into the framework, she takes Ophelia's place. Jemma doesn't remember the outside world once she's inside the framework, so only Daisy is self aware.Switches POV with each chapter.
Relationships: Leo Fitz/Jemma Simmons, Skye | Daisy Johnson/Grant Ward
Kudos: 18





	1. Madame Jemma

**Summary for the Chapter:**

> Jemma Simmons aka Madame Hydra's POV

**Notes for the Chapter:**

> Hi, yeah, I was re-reading the first chapter, and realized that it's shit, so I'm gonna re-write it right now, sorry :( 
> 
> Edit> So here it is, sorry it's short, but I have no attention span, and it was frustrating having to re-write it. //

I stuck my hand in the sensor, and waited for a beat, until the lab door clicked unlocked. I strode in, and shot a look towards one of the lower level agents, who scrambled out at my gaze.  
“Good morning Agent May, how’s the husband?” I said tossing the empty cup into the recycling bin.  
“He’s fine, Madame.” May said sitting up in her chair.  
“Melinda, you are one of the few people I trust, call me Jemma.” I collapsed into the chair next to my second in command. “Leopold.” I smiled and planted a feather light kiss on his cheek.  
“Yes Ma--” she stopped herself, “Of course, Jemma.” She seemed wildly uncomfortable using my first name. No one called me that, with the exception of Leo, my dad, his dad, and now Agent May and her husband.  
“Jemma, how’s Ward doing?” Leopold asked,  
Turning my attention back to the increasingly boring interrogation being performed by Agent Grant Ward.  
“Not great it seems.” I answered flatly. He was grasping at strings, but not pulling them too hard, and the subversive wasn’t giving anything away. Leopold may have to take control of this particular situation, he would get him to talk. “Blood samples for--” I picked up his portfolio, “Carter Grayson are running right now. May?” I asked, swiveling around in the chair.  
“Umm... Twelve more minutes.” She replied.  
“Great.” Leopold returned to tapping away at his computer, mumbling curses at the information he was reading.  
Right then, Leopold smashed his hand down onto the table.  
“Just as I thought…” He picked up his jacket and slipped his arms through it. He headed for the door.  
“What is it?” I asked, grabbing his hand before he could leave.  
He looked me in the eyes, “We have a mole.” His voice sounded like ice. “Lock down the building, Code Red, no one leaves without being vetted, there is an inside man, I repeat, there is an inside man.” He said into the announcement speaker on the wall. I followed him out, Melinda trailing not far behind after informing Ward.


	2. The Doctor

**Summary for the Chapter:**

> Leopold Fitz aka The Doctor's POV

**Notes for the Chapter:**

> I made yall wait for a VERY short chapter, so here is the next one :)

The halls were filled with Agents looking freakishly nervous and guilty. Me and Jemma rarely walk together. We usually have more pressing issues than workday chats, but today we are extra intimidating. There’s a wolf in the herd, and the people know what happens when that happens. Mostly because it’s happened before.  
About 2 years ago now, I was training a new intern, Ophelia Sarkissian. She had been part of S.H.I.E.L.D when it had fallen, but claimed her loyalties followed wherever the better paycheck was. Obviously, seeing she could care less for Hydra and all that it stood for, she was a risk. I decided that it would be best, if we kept her close to the top of the food chain. With more guards and security cameras, it was going to be difficult to pull any funny business. She went through every protocol for a new trainee, and passed. She was a decent fighter, but one of the best we had ever seen at doing undercover work (should’ve been the first red flag).  
After a few months of training, Jemma called her into her office randomly one day. Since I was her S.O., Jemma asked me to her office as well. I hadn’t thought much of it. People give faulty information on resumes all the time. But when we arrived there, Jemma was on the phone.  
“Okay, she’s right here, would you like to say hello? Lovely.” Jemma pushed the phone in Ophelia's direction and wore what was so obviously a fake smile. Ophelia took the phone and spoke at once, “Hello?” Her voice wavered through different pitches.  
“Ophelia! You said the encrypted line was secure! I thought that ‘secure’ meant, ya know, the head of Hydra couldn’t hack into it! MY MISTAKE! I gave you this assignment because you said you could handle it! So tell me what the hell is going on here!” The voice played loudly throughout the room.  
“Oops… I guess I forgot to tell you.” Jemma quietly laughed a little then whispered, “It’s on speaker phone.”.  
Later that day, Ophelia was sent through a Protocol known as ‘Hen in the Wolf house’. Basically it meant that they integrated her for hours on end, and when she wouldn’t talk, they executed her. They tried to decrypt the phone transmission to see if Agent Skye could trace the location, but no luck. 

We reach the briefing room two floors up. Whispers run through the small crowd that is around the conference table.  
“Agent Ward, is this everyone?” I look towards Ward, then glance around the room.  
“Yes, every Level 9 operative that is located in the Triskelion. Would you like me to send a Shelter In Place order to the other bases?”  
“You hadn’t already done that?” I asked.  
“No sir…”  
“Then do it, have Agent Skye,-- Where is Skye?” I say looking around the room then pin-pointing my gaze back on Ward.  
“I don’t know Doctor, she was acting strange this morning, I figured she was just late.” Ward pulls his phone, then puts it back in his pocket.  
I turned to Jemma, “Madame, you wouldn’t mind calling her, would you?” I ask, giving her an almost invisible smile.  
“Of course.” She returns the same fleeting grin, and I almost miss it. She turns to leave, but before she does she turns to Agent May. “Your husband, he’s a persuasive man, no?” she said looking at Melinda’s wedding ring then back up at her.  
“Yes, I mean he convinced me to settle down, so.” May laughed a little, and then read Jemma’s face, “I’ll call him in.” She said grabbing her phone off the table.  
“Lovely. Agent Rodgrigus, Agent Mackenzie, start bringing all level 1 and level 2 Agents into interrogation, let’s hope whoever is with S.H.I.E.L.D doesn’t have any higher clearance.” Jemma turned and walked out, dialling her phone in the process. May walked out behind her, already on a call with Mr. Coulson.  
It wouldn’t be good if the mole was a level 3 agent or higher, It takes about a year at the fastest to get that level, which would mean that he or she would’ve seen the beginning plans for many of our classified projects.  
I looked over every agent in the room. It seems just my gaze and them quiver out of fear.  
“If you let us down, there will be consequences.” I say through my teeth. Jemma plays favorites, has people she trusts, gives them room to breathe, more than others. I don’t. Everyone is a risk and everyone has secrets. Even me.


	3. Skye

**Summary for the Chapter:**

> POV of Skye/ Daisy Johnson

The loud ring of my phone makes my head pound. I pick up the device and check the name, to see if it's someone I know. The phone reads Madame Hydra.  
"Whoever calls themselves that needs to get a therapist..." I mumble to myself before answering the call. I hesitate, not knowing what to say, so I spit out the first thing that comes to mind.  
"Hail Hydra."  
"Agent Skye? Where the hell are you?!" The voice sounded sharp and rigid. And British.  
"Simmons?" I ask. I hear silence and then a small scoff from the other end.  
"Simmons?" She asks skeptically, "Skye, you may be on my good side, usually, but addressing me like any other agent is simply disrespectful." Her voice is filled with disgust. "Now if you would get down here now, we have a mole, and I need you to start running deeper profiles on the lower level agents." Simmons hangs up before letting me answer. I stare at the phone for a few seconds then get up from where I was sitting on me and Ward's bed. I walk over to the clothes thrown onto the desk, and briefly take in the picture sitting against the wall. I grab the clothes and begin to change into them. I can't think about THAT right now. Right now, My best friend is the head of hydra, and she has no idea who she really is, none of them do.  
\--  
I look back on older texts, and determine that I'm sanctioned at the Triskelion. I grab my phone and walk outside. The moment the wind blows on me, I wish I had brought a jacket. The air is chilled and leaves are falling off of trees. I walk to the road and wave down a cab. I climb into the backseat, and shut the door behind me.  
"The Triskelion, and make it quick, I'm late by like, an hour." I say.  
"Okay, but I hear there's a bit of commotion going on down there, you might wanna call in sick." He suggests, his New Jersey accent makes it almost impossible to decipher what he's saying.  
"That would make me look even more guilty that I already do." I breathe.  
Within a few minutes I see the building come into view, and the sight of it leaves an odd taste in my mouth.  
I drop a twenty into the cup holder in the front seat, and open the door of the taxi, "Keep the change." I shut the door and walk hastily into the establishment.  
When I get inside, There are a few Agents here and there, and one man in handcuffs being escorted out. One of the guards meets my curious glance, with an alarmed one.  
"You might want to hurry up, top brass has been talkin' about you, and I don't think it's about a Christmas bonus." He says as he leaves through the giant double glass doors I had come in through. I look out after him, then turn my attention back to the elevators that are now a few feet from me. I get on one. Floor? I'm about to pull out my phone when someone else gets on. I don't recognize them at first, but when I do, I can't get their face out of my mind. Miles.  
"What floor?" He asked, calmly. Guess he doesn't know me, then.  
"Where the briefing is." I say flatly, trying not to make eye contact with him. He presses a button that says '10th' on it, and the elevator doors close.  
\--  
When I walk into the briefing room, all heads swivel towards me. I smile awkwardly as I take in my co-workers. My eyes land on a familiar face. Fitz is sitting at the head of the conference table, looking over an Agents file. He takes notice of everyone's nervous glances towards something that isn't him or their work, and he looks up at me, making direct eye contact. The weight on my shoulders lifts off of me, only to come crashing down at his next words.  
"Agent Skye, if you wouldn't mind, would you please follow me to an interrogation room." He stands up and motions to the door. "Ladies first." he says plastering on one of the fakest smiles I've ever seen... ever. The mood in the room goes from SOS top brass is pissed to the sweet relief that she fucked up and not me.  
I sit down across from Fitz, trying to not look scared. Throw baby Fitz into a suit, and part his hair, and you have a terrifying, intimidating, if not slightly attractive head of Hydra.  
"How are things going with Ward." The way he says it let's me know that some feelings can't be shaken and he still hates him.  
"As good as you can expect." I reply, sitting up straight and looking around the room before my eyes settle on the ring on his finger.  
"Where's Madame Hydra." The words come out more sarcastic than I intended, and he takes notice, but brushes it off.  
"She's-" He stops to look at his watch "Coming here right now, actually. And you know you don't have to call her that. Her favorites call her Jemma" I can do Jemma, as long as I don't have to call him some stupid name.  
"But, still call me The Doctor." He says standing up from his chair. There goes my wish I think. He buttons a single button on his jacket, then walks behind my chair.  
“Ward told me that you were acting strange this morning. Then I discovered a mole within our ranks. It’s a bit odd, isn’t it?” He comes back into my view and leans over the table, waiting for an answer.  
“Sounds like a coincidence.” I say a little too quietly.  
“What’s that?” He points to his ears, “A bit louder.” he whispers.  
“Coincidence.” I repeat flatly.  
“Is it now.” He balances his chin on his hand and smiles a little. My skin crawls. How the hell is he so… creepy? When I change my hair, I don’t get a whole new personality. “Because it sounds more like you were caught in the middle, and maybe your boyfriend is defending you. Lying for you. Now that would have some serious consequences, wouldn’t ya think.” He walks over to the other side of the room, and fixes his hair in the one way mirror.  
Just then, Jemma walked in.  
“Madame.” Fitz smiled at her and she did too.  
“Doctor.” she touched his hand, briefly, before turning to me. “ It's come to my attention that you have been acting strangely, and with our call this morning, I can't disagree.” I shifted my weight. “Could you explain what happened to put you in such an awkward state?” Jemma sat in the seat that Fitz had vacated a few minutes before.  
“Well, Wa- Grant” I correct myself, not loving his name coming from my mouth, “He and I had a fight last night, so I didn’t get a lot of sleep.”  
“So you're tired?” Fitz asked, pulling up a stray chair, and seating himself next to his fiance.  
“Y- Yeah.” This felt weird. Wrong. I was being interrogated by my two best friends in a Hydra base. I want to go home.  
“Then how do you explain the other out of character behavior?” Jemma questioned, and Fitz continued for her. Pulling out a tablet, he swiped at the screen a few times, before turning it back to me. I recognized what he was displaying immediately. It was the DWARF and surveillance feeds.  
“You took a cab, despite having a car, you were drastically late, and you gawked at Agent Lydon like he got the promotion you wanted. Care to fill us in, because I’m willing to bet that you don’t want me to make an informed decision.” He set the device down, and leaned back, waiting for an answer.  
I glanced at the one-way glass. Someone was monitoring this. SHIELD had to be infiltrating Hydra, they always were, so, if I told the truth it might be broadcasted. It was a long shot. Like a fifteen mile away long shot, but I have no other way out of this. Hell was me best bet.  
“You have to believe me when I say this, okay? Please, don’t immediately assume I’m lying, consider what I’m saying.” FitzSimmons gave each other a look, then returned to staring at me.  
“Okay. This world isn’t real. You,” I gesture to a confused looking Fitz, “You designed a training program called ‘The Framework’, and Radcliff read a stupid book from hell, The Darkhold, and then he went crazy. He kidnapped you” I point to Fitz again, “May, Coulson, and Mack, and plugged you into this world he created so that Agnes could live, so she’s here too, probably. Aida needed Fitz to design her a body, because she was a robot, and she wants free will, so she can turn off the Framework, killing all of us. And- and I need your help to get out, because my way out is compromised by your dumb Hydra forces. I don’t know why you two are all evil, though if I’m being honest, it’s pretty attractive to see that side of you, but that’s not the point. The point is, that you need to believe me. Please.” I finished with a heavy sigh, and waited for the response.  
“That’s ludicrous.” Fitz said simply. “I want to know your whole fairy tale that you built, because I have to say it’s quite entertaining. But, I don’t have that time.” He looked to the one-way glass, and nodded his head. A pair of guards came in, and Fitz and Jemma stood to walk out.  
“Wait Fitz! Jemma! God. Um,” Say something that they would remember.  
“MAVETH!” I managed, before one of the men injected something into my arm, despite my struggling. The world spun for a moment, and then went dark.

**Notes for the Chapter:**

> uwu, this chapter is longer than both of the past ones combined, lets not think about it toooooo much lmao
> 
> Hope you enjoyed, I have to write the next chapter, so expect a few days for it to be up, because I am going back to school on Monday, so I have to do that stuff ahhhhhhhhh


	4. The Doctor

**Summary for the Chapter:**

> Ahhhhh inTerroGatiON

I stopped dead in my tracks. Maveth? What even is that? Why was it familiar? I turned back to Agent Skye, who was now being carried out. 

“Take her to the cells. I’d like to have a chat when she wakes up.” I said firmly. The men nodded and left. 

“What was that thing she said?” I picked up the almost invisible thread of worry in her voice. 

“Maveth.” I repeated. “Could you look it up, while I go ask her about it.” 

“Okay. And Leo,” I turned back to her, “Go easy with the pain. We want her to stay conscious.” I grinned at her in response. 

“I’ll try.” I turned and walked towards where the agents had moved Skye. I punch in the code, and hold my thumb over the scanner. When the door opens, I walk in. Skye was laying in the corner. 

I sat down on the rather uncomfortable chair, and waited for the dendrotoxin to wear off. Hydra rarely used the formula, only for subversives needed intact for questioning. 

It was a good twenty minutes later, when she finally let out a groan, and rolled over a bit. 

“Rise and shine.” I greeted her consciousness dryly. Skye let out another hiss of air when she heard me. She struggled to sit up, but she eventually leaned against the wall across from me. 

“What do you want?’ She had her hand on her head, most likely trying to ease off the headache that I knew she had from the sedative. 

“I want you to tell me about this reality” I air-quoted the last word. As much as I didn’t want to believe a word of it, things had always felt a little off. I would have vivid dreams, often involving the same people. A random assortment of agents, and his fiance. He hadn’t even known some of the peoples names until he looked them up. Agent Mackenzie, Agent Rodriguez, Agent May, Her husband, Agent Skye, and Jemma. 

He wouldn’t ever tell Jemma about it. Especially not now. That was the only thing he kept from her, and it ate him up. 

“I already did.”

“Then tell me more. If it’s a whole world. Whole lives, then there must be more. Try to convince me.” I persisted. 

Skye rolled her eyes. “Well, in the real world, you and Simmons are still together, but it did take you forever. Coulson and May have the hots for each other-”

“Mr. Coulson?” I interrupted. That was weird, how did she know him?

“You know him?”

“He’s Melinda’s husband.” I realized I sounded surprised, and purposefully made a mental not \e to keep my voice more nonchalant the next time I talked, “Is he part of the resistance too?” The resistance was a problem that Hydra couldn’t fix quite yet. They hid in the shadows, most citizens didn’t even know they existed, but inhumans and potential inhumans would go missing. That was the only way to know that they were active. 

“Not that I know. Anyway. You, Simmons, Ward, and May were all recruited for Coulson’s field team in the real world. You hated it, Jemma dragged you into it. Coulson picked me up after your first mission because I saved all your asses, one minor betrayal later, and I’m officially accepted into the cool kids squad. Then Ward turned out to be Hydra, and kinda dumped you two in the ocean.” She said the last part was significantly quieter. 

He had had nightmares about being underwater. Water rushing in. Knocking him out. His arm alway hurt significantly more than the rest of him in the dreams. Same arm he broke when he was younger, which is… strange. He was diagnosed with Thalassophobia when he was twenty two. 

“You had hypoxia, couldn’t speak without stumbling over your words. You couldn’t shave either, so you grew a little facial hair, which you never shaved again because Jemma is in love with it.” She smiled at a seemingly pleasant thought attached to that statement. 

“Jemma couldn't bear the thought of looking at you hurting. She pegged it as her fault that she took the last breath, so she went to work for Hydra.” 

“Wait. What!? She went to work for Hydra, when Ward was the reason that I was hurt, which is why Si- Jemma left?!” The grin Skye gave me, made me come to my wits, that I was way too into the false reality that former agent Skye was manipulating me with. I vow to show no more emotion for the rest of this chat that I’m now certain was going to conclude when the guards came off their lunch break.

“Yeah. You were pissed too. Probably the worst year for you guys, which is saying a lot.” I nodded, keeping my stoic expression. 

“Then Simmons got eaten by the Monolith after you had just asked her out. She was there for six months. Everyone gave up but you. When you got her back, she was denying that anything was wrong, all while trying to get back.”

“Back?” I cursed myself for being curious. 

“Yeah, she met some astro-dude. You went to Maveth, tried to get him back, but it turns out that his body was being controlled by the Hydra demon thing. He tried to kill you, but you totally kicked his ass. At least according to the team debrief.”

I was getting more and more angry with her constant insisting that this was my life. Mine and Jemma’s life. But this was my life. And I like my life. I have the girl of his dreams who challenges me, more wealth than I can spend in two lifetimes, and the respect of my father. 

I think I like my life. 

No. No I do. I like it. 

She continued. “Then I went under the sway of Hydra-zombie Ward, and hurt people.” Her voice went softer again. “And… Lincoln died for us.” It was barely noticeable in the dark room, but I could see her eyes glazed over at the name of someone who was obviously important to her. 

A weakness.

An exploit. 

“Lincoln?” I asked, leaning closer to look intrigued. She looked at me, hurt on her face. I felt bad for a second. But no. It wasn’t even real. It was fake hurt. She was trying to work with me. 

Two could play at that game. 

“Yeah. Anyway. Then you made a robot - ah and I went all goth, and ran away -, so you help Radcliffe build a robot thing, named AIDA. She went kill-crazy, but it turns out, it was Radcliff who went kill-crazy all for a dumb book.”

Book. A book that makes people go crazy. He knew a book like that. And it was in her cough-syrup world too. Exploit. 

“The Darkhold.” He interrupted. She flashed a quick smile. 

“Yeah.” 

“I remember.” I lied.

“You do?” I nodded,” Oh thank God, Fitz. We don’t have much time. We need to get out of this Hydra-Nazi plagued world!” She stood up wobbly. 

I walked with her to the door. A message from one of the guards chimed on my phone. 

‘What cell, Doctor?’ It read. I scowled, and responded. 

“Who’s that.” Skye asked. 

“Jemma.” I slipped it back in my pocket. 

I opened the door, and walked out with her. She knocked out the nearest agent, and took her gun. 

The guards were coming back. Skye pointed the weapon at them, about to fire, when a taser that was suddenly stuck to her side, made her collapse. 

She rolled over slightly, making eye contact with me. “Fitz?” She asked, weakly. 

I bent over, flicking a piece of hair out of her face. “Sorry agent Skye. But your wonder land will be a great gag for the news.” I stood back up, and gestured to the guards, who marched over, and picked her up. 

Knowing what was about to happen, she attempted to pull away from them, but to no avail, she could wriggle out of their grasp.

She settled for trying to talk her way out of this. “You don’t want to do this, Fitz.” 

He was content. “Yeah. I do.” They pulled her away, and a chorus of pleads rang in the air. 

“Guess you don’t know me at all.”

**Notes for the Chapter:**

> AHHH so short because I have no motivation for this any moreeeeeeee
> 
> I hope you liked this, but also this chapter is a little messed up, so if you overly-enjoyed it, you might wanna talk to someone about that.....
> 
> jk <3


End file.
